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Salt-responsive genes in rice revealed by cDNA microarray analysis

Cell Research 2005年第10期 50-64页

作者： Dai Yin CHAO1,3. Yong Hai LUO1,3. Min SHI1, Da LUO1,2, Hong Xuan LIN1,2,* 1National key laboratory of Plant molecular Genetics, Shanghai {3. of Plant Physiology and Ecology, Shanghai {3.s for Biological sciences, chinese academy of sciences, 3.0 Fenglin Road, Shanghai 20003., China, 2SHARF laboratory, Shanghai {3. of Plant Physiology and Ecology, Shanghai {3.s for Biological sciences, chinese academy of sciences, 3.0 Fenglin Road, Shanghai 20003., China, 3.raduate School of the chinese academy of sciences (D.C.), 19 Yuquan Road, Beijing 10003., China

We used cDNA microarrays containing ~9,000 unigenes to identify 486 salt responsive expressed sequence tags (ESTs) (representing ~450 unigenes) in shoots of the highly salt-tolerant rice variety, Nona Bokra (Oryza sativa L. ssp. Indica pv. Nona). Some of the genes identified in this study had previously been associated with salt stress. However the majority were novel, indicating that there is a great number of genes that are induced by salt exposure. Analysis of the salt stress expression profile data of Nona provided clues regarding some putative cellular and molecular processes that are undertaken by this tolerant rice variety in response to salt stress. Namely, we found that multiple transcription factors were induced during the initial salt response of shoots. Many genes whose encoded proteins are implicated in detoxification, protectant and transport were rapidly induced. Genes supporting photosynthesis were repressed and those supporting carbohydrate metabolism were altered. Commonality among the genes induced by salt exposure with those induced during senescence and biotic stress responses suggests that there are shared signaling pathways among these processes. We further compared the transcriptome changes of the salt-sensitive cultivar, IR28, with that of Nona rice. Many genes that are salt responsive in Nona were found to be differentially regulated in IR28. This study identified a large number of candidate functional genes that appear to be involved in salt tolerance and further examination of these genes may enable the molecular basis of salt tolerance to be elucidated.

关键词： cDNA microarray rice salt stress signaling crosstalk transcriptome.

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Lignin biosynthesis and its molecular regulation

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Progress in Natural Science:Materials International 2003年第5期 3-10页

作者： LIN Zhanbing, MA Qinghu and XU Yang(key laboratory of Photosynthesis and Environmental molecular Physiology, {3. of Botany, chinese academy of sciences, Beijing 100093. China) key laboratory of Photosynthesis and Environmental molecular Physiology Institute of Botany Chinese Academy of Sciences Beijing 100093 China

Lignin biosynthesis has become increasingly highlighted because it plays an important role in the growth and development of plant, in the systematic evolution of plant and in the human life. Due to the progress in the field of lignin studies in recent years, the lignin biosynthesis pathway has been revised. Here we discuss some genetic engineering approaches on lignin biosynthesis, and conceive strategy to regulate lignin biosynthesis in order to use lignin resource more efficiently in agricultural and industrial productions.

关键词： lignin biosynthesis molecular regulation genetic manipulation.

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Recombinant Neural Protein PrP Can Bind with Both Recombinant and Native Apolipoprotein E In Vitro

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Acta Biochimica et Biophysica Sinica 2006年第9期38卷 593-601页

作者： Chen GAO~1 Yan-Jun LEI~(1,2) Jun HAN~1 Qi SHI~1 Lan CHEN~(1,3. Yan GUO~(1,4) Yong-Jun GAO~1 Jian-Ming CHEN~1 Hui-Ying JIANG~1 Wei ZHOU~1 Xiao-Ping DONG~1* 1 State key laboratory for Infectious Disease Prevention and Control,National institute for Viral Disease Control and Prevention,{3. Center for Disease Control and Prevention,Beijing 100052,China 2 School of Medicine,Xi'an Jiaotong University,Xi'an 710061,China 3.National laboratory of Medical molecular Biology,institute of Basic Medical Science,{3. academy of Medical sciences and Peking Union Medical College,Beijing 100005,China 4 College of Science and Veterinary Medicine,Northwest Agriculture and Forest University,Yangling 712100,China State key laboratory for Infectious Disease Prevention and Control National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijing 100052 China School of Medicine Xi'an Jiaotong UniversityXi'an 710061 China National laboratory of Medical molecular Biology Institute of Basic Medical Science Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100005 China College of Science and Veterinary Medicine Northwest Agriculture and Forest UniversityYangling 712100 China

The most essential and crucial step during the pathogenesis of transmissible spongiformencephalopathy is the conformational change of cellular prion protein （PrPC） to pathologic isoform (PrPSc).Alot of data revealed that caveolae-like domains （CLDs） in the cell surface were the probable place where theconversion of PrP proteins *** E （ApoE） is an apolipoprotein which is considered toplay an important role in the development of Alzheimer's disease and other neurodegenerative diseases byforming protein complex through binding to the receptor located in the clathrin-coated pits of the cell *** this study,a 914-bp cDNA sequence encoding human ApoE3.was amplified from neuroblastoma cell *** human ApoE isomers were expressed and purified from Escherichia ***-specificantiserum was prepared by immunizing rabbits with the purified ***/His pull-down assay,immunoprecipitation and ELISA revealed that three full-length ApoE isomers interact with the recombinantfull-length PrP protein in *** regions corresponding to protein binding were mapped in the N-terminalsegment of ApoE （amino acid 1-194） and the N-terminal of PrP （amino acid 23.90）.Moreover,the recombinantPrP showed the ability to form a complex with the native ApoE from liver *** data provided directevidence of molecular interaction between ApoE and *** also supplied scientific clues for assessing thesignificance of CLDs on the surface of cellular membrane in the process of conformational conversion fromPrPCto PrPScand probing into the pathogenesis of transmissible spongiform encephalopathy.

关键词： prion disease PrP apolipoprotein E protein interaction caveolae-like domain

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Vertical adaptive radiation in ocean Prochlorococcus:evolutionary implications of the Ch1 b/a ratio from molecular evidence

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Progress in Natural Science:Materials International 2009年第11期19卷 1561-1568页

作者： Song Qin~(a,*),Yinchu Wang~(a,b) a Yantai institute of Coastal Zone Research for Sustainable Development,chinese academy of {3.,Yantai 264003.China b Graduate University of chinese academy of sciences,Beijing 100049,China Yantai institute of Coastal Zone Research for Sustainable Development Chinese Academy of Sciences Yantai 264003 China Graduate University of chinese academy of sciences Beijing 100049 China

Prochlorococcus is a marine cyanobacterium of global *** ecotypes are adapted to either high-light(HL) or low-light (LL) *** ratio between chlorophyll(Chl) a and b is a distinguishing characteristic of these two ***,how this ratio evolved in Prochlorococcus during this ecotype differentiation remains *** analyses reveal that the ancestor of Prochlorococcus was typically low-light *** LL ecotype showed a stagnant evolution,and the HL ecotype was recently *** was an adaptive radiation after directional evolution in the Chl bla ratio *** in chlorophyllide a oxygenase(CAO) and positive selection on Clp protease contributed to the directional evolution of *** recombinant fragments of CAO were correlated with a large group of shared coevolving *** of positive selection was found in both subunits of *** bla ratio evolution,as annotated by molecular evidence,appears to be among the crucial reasons that explain how Prochlorococcus has become the dominant photosynthetic organism in the ocean.

关键词： Prochlorococcus Ch1 b/a ratio Adaptive evolution Trait evolution Ecotype differentiation

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molecular evolution and phylogeny of the angiosperm ycf2 gene

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Journal of Systematics and evolution 2010年第4期48卷 240-248页

作者： 1 Jin-Ling HUANG 1Gui-Ling SUN 2Da-Ming ZHANG 1(Department of Biology,East Carolina University,Greenville,NC 27858,USA) 2(State key laboratory of Systematic and evolutionary Botany,{3. of Botany,chinese academy of sciences,Beijing 100093.China) (Department of Biology East Carolina University Greenville NC 27858 USA) (State key laboratory of Systematic and evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China)

Much of the recent progress in understanding angiosperm phylogeny has been achieved using multigene or plastid genome ***,it is largely unclear what size of dataset is required to achieve sufficient *** ycf2 gene is the largest plastid gene in angiosperms and it was used as part of multigene datasets in several earlier investigations into angiosperm *** this study,we show that the ycf2 gene alone can provide a generally well-supported phylogeny that is consistent with those inferred from the most comprehensive multigene or plastid genome *** phylogenetic signal of the ycf2 gene is likely derived from the combination of its long sequence length and low rate of nucleotide *** ycf2 gene may provide a low-cost alternative to comprehensive multigene or genome datasets for investigating angiosperm relationships.

关键词： angiosperm phylogeny indel multigene dataset molecular evolution

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An embryological study and systematic significance of the primitive gymnosperm Ginkgo biloba

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Journal of Systematics and evolution 2011年第4期49卷 353-361页

作者： 1,2Li WANG 1Di WANG 1Ming-Ming LIN 1Yan LU 1Xiao-Xue JIANG 1Biao JIN 1(College of Horticulture and Plant Protection,Yangzhou University,Yangzhou 225009,China) 2(key laboratory of Photosynthesis and Environmental molecular Physiology,{3. of Botany,chinese academy of sciences,Beijing 100093.China) (College of Horticulture and Plant Protection Yangzhou University Yangzhou 225009 China) (key laboratory of Photosynthesis and Environmental molecular Physiology Institute of Botany Chinese Academy of Sciences Beijing 100093 China)

Ginkgo biloba *** considered one of the most ancient seed plants,with several primitive features of plant reproductive ***,the phylogenetic position of Ginkgo and its relationship with other extant seed plants remain *** gain a better understanding of these issues,we observed the embryological development of *** using semi-thin sections and scanning electron *** late August,the zygote moved from the end of the micropylar to the middle of the archegonium,and mitosis resulted in many free nuclei distributed randomly in the ***,the cell wall was formed and the proembryo began to differentiate into the embryonal region and the underdeveloped presuspensor *** early October,the embryo differentiated into two cotyledons,plumule,hypocotyl,radicle,and suspensor ***,the two cotyledons grew rapidly,but the undeveloped suspensor began to degenerate and gradually disappear,indicating that the embryo had begun to *** early embryo development,the main supply of nutrients was carbohydrate in the cells of the jacket,tentpole,and surrounding endosperm,whereas endosperm provided nutrients during embryo *** results indicate that Ginkgo is extremely similar to cycads in terms of embryology but more similar to conifers in macromorphology and vegetative anatomy,suggesting that the Ginkgo lineage may have an intermediate phylogenetic position between cycads and conifers.

关键词： embryo development Ginkgo biloba L. systematic significance.

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Dichloroacetic acid and rapamycin synergistically inhibit tumor progression

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2023年第5期24卷 397-405页

作者： Huan CHEN kunming LIANG Cong HOU Hai-long PIAO CAS key laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China Department of Biochemistry&molecular Biology School of Life SciencesChina Medical UniversityShenyang 110122China University of chinese academy of sciences Beijing 100049China

Mammalian target of rapamycin(mTOR)controls cellular anabolism,and mTOR signaling is hyperactive in most cancer *** a result,inhibition of mTOR signaling benefits cancer *** is a US Food and Drug Administration(FDA)-approved drug,a specific mTOR complex 1(mTORC1)inhibitor,for the treatment of several different types of ***,rapamycin is reported to inhibit cancer growth rather than induce *** dehydrogenase complex(PDHc)is the gatekeeper for mitochondrial pyruvate *** inactivation has been observed in a number of cancer cells,and this alteration protects cancer cells from senescence and nicotinamide adenine dinucleotide(NAD^(+))*** this paper,we describe our finding that rapamycin treatment promotes pyruvate dehydrogenase E1 subunit alpha 1(PDHA1)phosphorylation and leads to PDHc inactivation dependent on mTOR signaling inhibition in *** inactivation reduces the sensitivity of cancer cells'response to *** a result,rebooting PDHc activity with dichloroacetic acid(DCA),a pyruvate dehydrogenase kinase(PDK)inhibitor,promotes cancer cells'susceptibility to rapamycin treatment in vitro and in vivo.

关键词： Dichloroacetic acid(DCA) Rapamycin Pyruvate dehydrogenase E1 subunit alpha 1(PDHA1) Mammalian target of rapamycin(mTOR)

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A model to predict phase equilibrium of CH4 and CO2 elathrate hydrate in aqueous electrolyte solutions

A model to predict phase equilibrium of CH4 and CO2 elathrat...

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中国科学院地质与地球物理研究所2006学术年会

作者： Zhenhao Duan~* and Rui Sun State key laboratory of Lithospheric evolution,{3. of Geology and Geophysics,chinese academy of sciences,Beijing,100029,China

A thermodynamic model to predict phase equilibrium of methane and carbon dioxide hydrate in aqueous electrolyte solutions is *** the Pitzer model to account for the variation of water activity due to electrolytes and dissolved gas in aqueous solutions,we extended the model based on ab initio molecular potential developed recently by us for the CH-HO and CO-HO binary systems to the CH(or CO-HO-salts *** of the model with extensive experimental data indicates that this model can accurately predict the phase equilibrium of CH hydrate and CO hydrate in various electrolyte solutions(such as aqueous NaCl,KCl, CaCl,NaCl + KCl,NaCl + CaCl solutions,and seawater) from zero to high ionic strength(about 6 m) and from low to high pressures.

关键词： Methane hydrate carbon dioxide hydrate thermodynamic stability electrolyte solution phase equilibrium formation conditions

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Equation of state of the H2O,CO2,and H2O-CO2 systems up to 10 GPa and 2573.15 K:molecular dynamics simulations with ab initio potential surface

Equation of state of the H2O,CO2,and H2O-CO2 systems up to 1...

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中国科学院地质与地球物理研究所2006学术年会

作者： Zhenhao Duan~*,Zhigang Zhang State key laboratory of Lithospheric evolution,{3. of Geology and Geophysics,chinese academy of sciences,Beijing,100029,China

Based on our previous development of the molecular interaction potential for pure HO and CO[Zhang,Z.G.,Duan,***-isobaric molecular dynamics simulations of the PVT properties of water over wide range of temperatures and ***. Earth Planet Interiors 149,3.5-3.4;Zhang,Z.G,Duan,*** optimized molecular potential for carbon ***.122,214507]and the ab initio potential surface across CO-HO molecules constructed in this study,we carried out more than one thousand molecular dynamics simulations of the PVTx properties of the CO-HO mixtures in the temperature-pressure range from 673.15 to 2573.15 K up to 10.0 *** with extensive experimental PVTx data indicates that the simulated results generally agree with experimental data within 2%in density,equivalent to experimental *** the data under the highest experimental temperature-pressure conditions(up to 1673.K and 1.94 GPa) are well predicted with the agreement within 1.0%in density,indicating that the high accuracy of the simulation is well retained as the temperature and pressure *** consistent and stable predictability of the simulation from low to high temperature-pressure and the fact that the molecular dynamics simulation resort to no experimental data but to ab initio molecular potential makes us convinced that the simulation results should be reliable up to at least 2573.K and 10 GPa with errors less than 2%in *** order to integrate all the simulation results of this study and previous studies [Zhang and Duan,2005a,2005b]and the experimental data for the calculation of volumetric properties(volume,density,and excess volume),heat properties,and chemical properties(fugacity, activity,and possibly supercritical phase separation),an equation of state(EOS) is laboriously developed for the CO,HO,and CO-HO *** EOS reproduces all the experimental and simulated data covering a wide temperature and pressure range from 673.15 to 2573.

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Developing a microfluidic-based system to quantify cell capture efficiency

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Science China(Life sciences) 2009年第2期52卷 173-181页

作者： YANG Fan, GAO YuXin, ZHANG Yan, CHEN Juan & LONG Mian National Microgravity laboratory and Center for Biomechanics and Bioengineering, institute of Mechanics, chinese academy of sciences, Beijing 100080, China National Microgravity laboratory and Center for Biomechanics and Bioengineering Institute of Mechanics Chinese Academy of Sciences Beijing China

Micro-fabrication technology has substantial potential for identifying molecular markers expressed on the surfaces of tissue cells and viruses. It has been found in several conceptual prototypes that cells with such markers are able to be captured by their antibodies immobilized on microchannel substrates and unbound cells are flushed out by a driven flow. The feasibility and reliability of such a microflu- idic-based assay, however, remains to be further tested. In the current work, we developed a microflu- idic-based system consisting of a microfluidic chip, an image grabbing unit, data acquisition and analysis software, as well as a supporting base. Specific binding of CD59-expressed or BSA-coupled human red blood cells (RBCs) to anti-CD59 or anti-BSA antibody-immobilized chip surfaces was quan- tified by capture efficiency and by the fraction of bound cells. Impacts of respective flow rate, cell concentration, antibody concentration and site density were tested systematically. The measured data indicated that the assay was robust. The robustness was further confirmed by capture efficiencies measured from an independent ELISA-based cell binding assay. These results demonstrated that the system developed provided a new platform to effectively quantify cellular surface markers effectively, which promoted the potential applications in both biological studies and clinical diagnoses.

关键词： cell surface marker microfluidic capture efficiency

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